Aligning protein sequences using Muscle through Perl

Question

[Andrea]

I get this error when i m running this script:

Code

#!/usr/bin/perl

use strict;

use warnings;

use Bio::Tools::Run::Alignment::Muscle;

# Build a muscle alignment factory

my @params = ( -outfile_name => 'outfile.fa' );

my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);

# Pass the factory a list of sequences to be aligned .

my $inputfilename = 'sequence.fasta';

# $aln is a SimpleAlign object .

my $aln = $factory->align( $inputfilename );

exit;

Error message:

'-in' not recognized as an internal or external command,

executable program or script file.

--------------------- WARNING ---------------------MSG: Muscle call crashed: 256 [command -in sequence.fa -out outfile.fa]---------------------------------------------------

Any clue pleaze???

[Josh Herr]

A Perl code of 256 (I think) means an exit code of $1 -- is this an error concerning your input file? Is muscle working in your path? Is there an error in your code such that the output of the first part of your code is not being passed to muscle?